In a
New York Times op-ed, Gunn explains how it's normal for the
viewer to empathize with and root for Walt since he's the show's
protagonist. Since her reactions go against Walt, she's easily
seen as a foe even though she's acing in a rational
manner.

Here's part of her response to the message board
haters:

"As an actress, I realize that viewers are entitled to have
whatever feelings they want about the characters they watch. But
as a human being, I’m concerned that so many people react to
Skyler with such venom. Could it be that they can’t stand a woman
who won’t suffer silently or “stand by her man”? That they
despise her because she won’t back down or give up? Or because
she is, in fact, Walter’s equal?"

In the end, Gunn decided it comes down to gender.

"But I finally realized that most people’s hatred of Skyler had
little to do with me and a lot to do with their own perception of
women and wives. Because Skyler didn’t conform to a comfortable
ideal of the archetypical female, she had become a kind of
Rorschach test for society, a measure of our attitudes toward
gender."